TarDB: A miRNA Target Database in Plants.


TarDB employs cross-species conservation filter, degradome and sRNA-seq data to identify high-confidence miRNA targets in plants.



miRNA ID

mdm-miR408c

Organism

Malus domestica

Species

Mature miRNA Sequence(5'-3')

ACAGGGAAGAGGUAGAGCAUG

miRBase

Precursor miRNA Sequence(5'-3')

AAGUAUUUGAGUAAUGCGGAAAGAGAGUUAAUAAGACAGGGAAGAGGUAGAGCAUGGAUGGAGUUCUCAAGAGCAAAAUAGAGCUCUUGUGACUCUACUCAUGCACUGCCURUUCCCUGGCUUUGCCUCCCUCUCCUUCCUUUUUCUCAUCCUCUU

miRBase

Precursor miRNA Structure(5'-3') 

   UAUU    U  UGC    A     --UUAAU   A       G      A      A       CU       AAA 
AAG    UGAG AA   GGAA GAGAG       AAG CAGGGAA AGGUAG GCAUGG UGGAGUU  CAAGAGC   A
|||    |||| ||   |||| |||||       ||| ||||||| |||||| |||||| |||||||  |||||||    
UUC    ACUC UU   CCUU CUCUC       UUC GUCCCUU UCCGUC CGUACU AUCUCAG  GUUCUCG   G
   UCCU    -  UUU    C     CCUCCGU   G       R      A      C       -U       AGA

Homologous Mature miRNAs   miRNAs are clustered by CD-HIT with sequence identity of >85% and word size of 5.

ath-miR408-5p       ACAGGGAACAAGCAGAGCAUG-
aly-miR408-5p       -CAGGGAACAAGCAGAGCAUGG
mtr-miR408-5p       ACAGGGAACAUGCAGAGCAUG-
mdm-miR408b         ACAGGGAAGAGGUAGAGCAUG-
mdm-miR408c         ACAGGGAAGAGGUAGAGCAUG-
mdm-miR408d         ACAGGGAAGAGGUAGAGCAUG-
gma-miR408a-5p      CAGGGGAACAGGCAGAGCAUG-
gma-miR408c-5p      CAGGGGAACAGGCAGAGCAUG-
ptc-miR408-5p       -CGGGGAACAGGCAGAGCAUGG
csi-miR408-5p       ACGGGGAACAGGCAGAGCAUG-
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